Merge branch 'master' into posix-lf

Author: salim-b

.Rbuildignore

@@ -21,3 +21,5 @@ README.Rmd
 abbvie.R
 ^\.httr-oauth$
 ^\.github$
+^\.venv$
+CLAUDE\.md

.github/workflows/R-CMD-check.yaml

@@ -34,7 +34,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          # - {os: ubuntu-latest,   r: 'oldrel-3'} # dependency issues with oldrel-3
           # - {os: ubuntu-latest,   r: 'oldrel-4'} # dependency issues with oldrel-4
 
     env:
@@ -72,7 +72,8 @@ jobs:
       - name: Install kaleido
         if: matrix.config.visual_tests == true
         run: |
-          Rscript -e 'library(reticulate); use_python(Sys.which("python")); py_install(c("kaleido", "plotly"))'
+          # We pin kaleido to v0.2.1 here since >=v1.0 doesn't appear to be correctly rendering some plots
+          Rscript -e 'library(reticulate); use_python(Sys.which("python")); py_install(c("kaleido==0.2.1", "plotly"))'
         
         # Run test() before R CMD check since, for some reason, rcmdcheck::rcmdcheck() skips vdiffr tests
       - name: Run Tests

.github/workflows/docs.yml

@@ -0,0 +1,74 @@
+# Add this file to plotly/plotly.R at .github/workflows/docs.yml
+#
+# This workflow builds and deploys the R documentation site from
+# the graphing-library-docs repository to this repo's GitHub Pages.
+
+name: Deploy R Documentation
+
+on:
+  # Manual trigger
+  workflow_dispatch:
+
+  # Run weekly to pick up any docs changes
+  schedule:
+    - cron: '0 0 * * 0'  # Every Sunday at midnight UTC
+
+  # Optional: trigger from docs repo via repository_dispatch
+  repository_dispatch:
+    types: [docs-updated]
+
+# Sets permissions for GitHub Pages deployment
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+env:
+  # Change this if the docs repo moves to a different location
+  DOCS_REPO: cpsievert/graphing-library-docs
+  DOCS_BRANCH: master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout docs repository
+        uses: actions/checkout@v4
+        with:
+          repository: ${{ env.DOCS_REPO }}
+          ref: ${{ env.DOCS_BRANCH }}
+
+      - name: Setup Ruby
+        uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: '3.2'
+          bundler-cache: true
+
+      - name: Fetch R/ggplot2 docs from plotly.r-docs
+        run: make fetch
+
+      - name: Build site
+        run: bundle exec jekyll build --config _config.yml,_config_production.yml
+        env:
+          JEKYLL_ENV: production
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _site
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -4,6 +4,7 @@ Rapp.history
 *.RData
 *.Rproj.user
 *.DS_Store
+.venv
 node_modules/
 build_site.R
 revdep_email.R
@@ -18,3 +19,4 @@ revdep/
 travis_debug.R
 .httr-oauth
 tests/testthat/Rplots.pdf
+.venv/

CLAUDE.md

@@ -0,0 +1,98 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+plotly is an R package for creating interactive web graphics via the plotly.js JavaScript library. It provides two main interfaces:
+- `ggplotly()`: Converts ggplot2 objects to interactive plotly visualizations
+- `plot_ly()`: Direct interface to plotly.js for specialized chart types
+
+## Common Commands
+
+### Running Tests
+```r
+# Run all tests
+devtools::test()
+
+# Run visual tests (requires kaleido via reticulate)
+Sys.setenv("VISUAL_TESTS" = "true")
+devtools::test()
+
+# Run a single test file
+devtools::test(filter = "ggplot-bar")
+```
+
+### Package Check
+```r
+rcmdcheck::rcmdcheck()
+```
+
+### Building Documentation
+```r
+devtools::document()
+```
+
+### Visual Testing via Docker
+For consistent visual test results:
+```shell
+docker run -v $(pwd):/home/plotly --privileged -p 3838:3838 cpsievert/plotly-orca
+```
+Access the validation Shiny app at http://0.0.0.0:3838
+
+CI-only visual test run:
+```shell
+docker run -e VMODE="ci" -v $(pwd):/home/plotly --privileged cpsievert/plotly-orca
+```
+
+## Architecture
+
+### ggplot2 to plotly Conversion Pipeline
+
+The conversion from ggplot2 to plotly follows this flow:
+
+1. **`ggplotly()`** (`R/ggplotly.R`): Entry point that dispatches on input type
+2. **`gg2list()`** (`R/ggplotly.R`): Main conversion function that:
+   - Builds the ggplot object to extract computed data
+   - Processes each layer through `layers2traces()`
+   - Processes layout through `layers2layout()`
+3. **`layers2traces()`** (`R/layers2traces.R`): Converts ggplot2 geom layers to plotly trace objects
+4. **`layers2layout()`** (`R/layers2layout.R`): Converts ggplot2 theme/coordinate settings to plotly layout
+
+### Direct plotly Interface
+
+1. **`plot_ly()`** (`R/plotly.R`): Creates a plotly object with trace attributes
+2. **`add_trace()`** and `add_*()` functions (`R/add.R`): Add traces to existing plots
+3. **`layout()`** (`R/layout.R`): Modify plot layout
+4. **`plotly_build()`** (`R/plotly_build.R`): Evaluates lazy attributes and creates final JSON for plotly.js
+
+### Key Modules
+
+- `R/shiny.R`: Shiny integration and event handling
+- `R/subplots.R`: Combining multiple plots
+- `R/highlight.R`: Linked brushing/crosstalk support
+- `R/animate.R`: Animation support
+- `R/kaleido.R`, `R/orca.R`: Static image export
+
+## Testing Patterns
+
+Tests should check the return value of `plotly_build()`:
+```r
+test_that("example test", {
+  p <- plot_ly(x = 1:10, y = 1:10)
+  built <- plotly_build(p)
+  expect_equal(built$x$data[[1]]$x, 1:10)
+})
+```
+
+Visual tests use `expect_doppelganger()` from `tests/testthat/helper-vdiffr.R`:
+```r
+test_that("visual test", {
+  p <- plot_ly(x = 1:10, y = 1:10)
+  expect_doppelganger(p, "scatter-basic")
+})
+```
+
+## Code Style
+
+Follow the tidyverse style guide: http://style.tidyverse.org/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: plotly
 Title: Create Interactive Web Graphics via 'plotly.js'
-Version: 4.11.0
+Version: 4.12.0.9000
 Authors@R: c(person("Carson", "Sievert", role = c("aut", "cre"),
     email = "cpsievert1@gmail.com", comment = c(ORCID = "0000-0002-4958-2844")),
     person("Chris", "Parmer", role = "aut",
@@ -78,7 +78,7 @@ Suggests:
     rsvg,
     ggridges
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/Needs/check:

NAMESPACE

@@ -32,6 +32,7 @@ S3method(linewidth_or_size,default)
 S3method(linewidth_or_size,element)
 S3method(plotly_build,"NULL")
 S3method(plotly_build,gg)
+S3method(plotly_build,ggmatrix)
 S3method(plotly_build,list)
 S3method(plotly_build,plotly)
 S3method(print,api)

NEWS.md

@@ -1,3 +1,44 @@
+# plotly (development version)
+
+
+
+
+# plotly 4.12.0
+
+## Changes to plotly.js
+
+Upgrades plotly.js from v2.11.1 to v2.25.2 (35 releases). Key new features now available:
+
+* **Multiple legends**: Support for `legend2`, `legend3`, etc. with separate positioning and visibility control
+* **Shape labels**: New `label` attribute for shapes and `label.texttemplate` for parametric shapes
+* **Marker direction**: New `marker.angle`, `marker.angleref`, and `marker.standoff` properties for directional markers
+* **Y-axis positioning**: `shift` and `autoshift` properties to avoid y-axis overlapping in multi-axis plots
+* **Mapbox clustering**: Clustering options and bounds support for `scattermapbox` traces
+* **Equal Earth projection**: New map projection option for geo subplots
+* **Pattern fills**: Pattern support extended to pie, funnelarea, sunburst, icicle, and treemap charts
+* **Editable selections**: Persistent and editable selections over cartesian subplots with `editSelection` config option
+* **Axis label aliases**: `labelalias` for simplified axis label customization
+* **Grid styling**: `griddash` property and minor tick/grid line styling options
+
+Also includes a security fix for prototype pollution and ~90KB bundle size reduction.
+
+See the [plotly.js releases page](https://github.com/plotly/plotly.js/releases) for the full changelog.
+
+## Improvements
+
+* `save_image()` now works with kaleido v1.0 and higher. (#2447)
+
+## Bug fixes
+
+* `plotly_build()` now works with `ggmatrix` objects (e.g., from `GGally::ggpairs()`). (#2447)
+* Closed #2415: `ggplotly()` now shows variables named 'group' in tooltips when mapped to aesthetics like `colour`.
+* Closed #2455, #2460: `ggplotly()` no longer creates empty shapes when `panel.border` is `element_blank()` (ggplot2 4.0.0 compatibility).
+* Closed #2466: `ggplotly()` no longer errors when `scale_*_manual()` has unused aesthetics (e.g., `aesthetics = c("colour", "fill")` when only colour is used).
+* Closed #2305: `ggplotly()` now respects `geom_boxplot(outlier.shape = NA)` to hide outlier points.
+* Closed #2467: `ggplotly()` now correctly shows legends and splits traces when scales have multiple aesthetics.
+* Closed #2407, #2187: `ggplotly()` now translates `legend.position` theme element to plotly layout (supports "bottom", "top", "left", and numeric positions).
+* Closed #2281: `ggplotly()` no longer drops legends when `geom_blank()` is present in the plot.
+
 # plotly 4.11.0
 
 ## New features
@@ -369,7 +410,7 @@ This is minor patch release with a few minor bug fixes and updates test expectat
 * Added the `highlight()` function for configuring selection modes/sequences/options.
 * Added support for animation. For some relatively basic examples, see the examples section of `help(animation)`. For a more thorough overview, see <https://plotly-r.com/animating-views.html>
 * Added a `frame` argument to `plot_ly()` for creating animations. Also added the `animation_opts()`, `animation_slider()`, and `animation_button()` functions for configuring animation defaults.
-* Added a new interface to [v2 of the REST API](https://api.plot.ly/v2). This new interface makes the  `plotly_POST()` and `get_figure()` functions obsolete (use `api_create()` and `api_download_plot()` instead), and thus, are now deprecated, but remain around for backwards-compatibility. For more details, see `help(api)`.
+* Added a new interface to v2 of the REST API. This new interface makes the  `plotly_POST()` and `get_figure()` functions obsolete (use `api_create()` and `api_download_plot()` instead), and thus, are now deprecated, but remain around for backwards-compatibility. For more details, see `help(api)`.
 * Added support for conversion of more **ggplot2** geoms via `ggplotly()`: `GeomCol`, `GeomRug`, `GeomCrossbar`, `GeomQuantile`, `GeomSpoke`, `GeomDotplot`, `GeomRasterAnn` (i.e., `annotation_raster()`), and `GeomAnnotationMap` (i.e., `annotation_map()`).
 * Added a new function `raster2uri()` which makes it easier to embed raster objects as [images](https://plotly.com/r/reference/#layout-images) via data URIs. For examples, see `help(raster2uri)`.
 * `ggplotly()` gains a new argument, `dynamicTicks`, which allows axis ticks to update upon zoom/pan interactions (fixes #485).
@@ -1146,7 +1187,7 @@ Fixed filename, fileopt arguments in plot_ly. Specifying the same filename will
 
 1.0.8 -- 14 Sep 2015
 
-Added the plotly_IMAGES() function which interfaces to the images endpoint https://api.plot.ly/v2/#images
+Added the plotly_IMAGES() function which interfaces to the images endpoint.
 
 Details -> https://github.com/ropensci/plotly/pull/279
 

R/api_exports.R

@@ -44,7 +44,6 @@
 #' @export
 #' @rdname api
 #' @author Carson Sievert
-#' @references \url{https://api.plot.ly/v2}
 #' @seealso [signup()]
 #' @examplesIf interactive() || !identical(.Platform$OS.type, "windows")
 #' 
@@ -80,30 +79,29 @@
 #' api()
 #' 
 #' # search the entire platform!
-#' # see https://api.plot.ly/v2/search
 #' api("search?q=overdose")
 #' api("search?q=plottype:pie trump fake")
 #' 
 #' # these examples will require a user account
 #' usr <- Sys.getenv("plotly_username", NA)
 #' if (!is.na(usr)) {
-#'   # your account info https://api.plot.ly/v2/#users
+#'   # your account info
 #'   api(sprintf("users/%s", usr))
-#'   # your folders/files https://api.plot.ly/v2/folders#user
+#'   # your folders/files
 #'   api(sprintf("folders/home?user=%s", usr))
 #' }
 #' 
-#' # Retrieve a specific file https://api.plot.ly/v2/files#retrieve
+#' # Retrieve a specific file
 #' api("files/cpsievert:14681")
-#' 
-#' # change the filename https://api.plot.ly/v2/files#update
+#'
+#' # change the filename
 #' # (note: this won't work unless you have proper credentials to the relevant account)
-#' api("files/cpsievert:14681", "PATCH", list(filename = "toy file")) 
-#' 
-#' # Copy a file https://api.plot.ly/v2/files#lookup
+#' api("files/cpsievert:14681", "PATCH", list(filename = "toy file"))
+#'
+#' # Copy a file
 #' api("files/cpsievert:14681/copy", "POST")
-#' 
-#' # Create a folder https://api.plot.ly/v2/folders#create
+#'
+#' # Create a folder
 #' api("folders", "POST", list(path = "/starts/at/root/and/ends/here"))
 #' 
 #' }